Various biosignals (neurotransmitters, hormones, cytokines) generated from extracellular signal transduction systems networked in the body (nervous system, endocrine system, immune system) are received and transmitted by intracellular signal transduction systems in target cells, resulting in appropriate responses. Here, the majority of biosignals are transmitted by protein-to-protein interactions. For example, various protein-to-protein interactions are involved in the binding of cell surface receptors and specific ligands therefor, and also in intracellular signal transduction from cytoplasm to nucleus. Therefore, disorders and abnormalities of intracellular signal transduction systems are closely associated with the pathogenesis of many serious diseases. Against this background, it is an urgent demand to create molecules capable of controlling (promoting or suppressing) protein-to-protein interactions as targets. At present, as a means of elucidating protein-to-protein interactions such as ligand-receptor interactions, and as a means of treating diseases resulting from signal cascade abnormalities, physiologically active peptides capable of interacting with target proteins are under active research and development.
Physiologically active peptides play an important role in controlling various physiological functions as signal transmitters in the body. However, in nature, physiologically active peptides occur only in trace amounts and are very difficult to purify; only less than 100 have been discovered to date. On the other hand, with the construction of genome databases, it is supposed that there are a significant number of orphan receptors deemed physiologically active peptide receptors, and searching ligands therefor is an important key to new drug development. As examples of peptide pharmaceuticals in clinical application or under development, there may be mentioned 1) hypothalamic hormone derivatives, 2) posterior pituitary hormone derivatives, 3) ANP derivatives, 4) calcium-regulating hormones, 5) peptide antibiotics, etc. Additionally, new physiologically active peptides have recently been discovered using cells that were allowed to express orphan receptors. Using this technique, Takeda Chemical Industries discovered metastin, a peptide ligand for an orphan receptor that suppresses cancer metastasis (see, for example, Nature, 411, 613 (2001)). It is expected that further investigations in search for other physiologically active peptides will be undertaken, resulting in the development of valuable peptide pharmaceuticals.
However, no effective methodology remains established to predict the amino acid sequence of a peptide capable of binding to and interacting with an optionally chosen amino acid sequence of protein; it is common practice to screen for physiologically active peptides by biochemical techniques. For example, there may be used a technique wherein a plurality of consecutive peptides consisting of 10-20 amino acids from the N-terminus to the C-terminus are synthesized from a protein known to bind to another protein, from among which peptides a physiologically active peptide is selected, or a technique wherein a physiologically active peptide is selected from a randomized peptide library using a phage library. However, such biochemical methods have been problematic in that much costs and time are required. Hence, there has been a demand for the development of a technique for both theoretically and more economically and conveniently designing a physiologically active peptide, rather than a conventional technique.
On the other hand, some theories to predict a physiologically active peptide sequence for target amino acid sequence have been proposed to date. Watson and Crick set forth the DNA strand model and asserted that base pairs existed but amino acid pairs did not exist; however, there had been the minority opinion that amino acid pairs might exist (see, for example, Journal of Theoretical Biology, vol. 94, p885-894 (1982)).
The sense-antisense theory, advocated by Blalock et al. (see, for example, Biochemical Biophysical Research Communication, vol. 121, p203-207 (1984)) is also premised on amino acid pairs, its contents being based on the hypothesis that two peptides encoded by two complementary DNAs, like bases, interact with each other. Based on this theory, it has been confirmed experimentally that some antisense peptides interact with sense peptides.
On the other hand, in response to the suggestion of Blalock et al. that sense peptides and antisense peptides are high in <complementariness in terms of the degree of hydrophobicity>, Fassina et al. showed in some experiments that a complementary peptide having a degree of hydrophobicity that is complementary (sharing the same absolute value, but having the reverse positive/negative sign) to the average degree of hydrophobicity of five or more consecutive odd-numbered amino acids in a peptide binds to the original peptide (see, for example, Archives of Biochemistry and Biophysics, vol. 296, 137-143 (1992)). However, numerous cases of failures have been reported for all these theories, the theories cannot be said to be satisfactory for the application to the prediction of common physiologically active peptides. Also, in all these theories, a plurality of amino acid candidates are available for each amino acid of target amino acid sequence; a vast number of candidate peptides are predicted, examining all of which takes vast amounts of time, costs, and labor.
Additionally, even if succeeding in obtaining a physiologically active peptide comprising an amino acid sequence that interacts with a target amino acid sequence, we encounter further problems. As target sites of protein to be targeted in drug innovation, there may be mentioned ligand binding sites (e.g., in the case of receptors), substrate binding sites (e.g., in the case of enzymes), protein-to-protein interaction sites (e.g., in the case of transcription factors, multimer-(e.g., dimer)-forming proteins), etc.; however, these target sites very often comprise a plurality of partial amino acid sequences localized apart on the primary structure, rather than of a single consecutive amino acid sequence. Therefore, even if a physiologically active peptide comprising an amino acid sequence that interacts with a target amino acid sequence is obtained, the amino acid sequence is often not preferable for other amino acid sequences present at the target site.
Additionally, provided that a target site of target protein comprises a plurality of partial amino acid sequences localized apart on the primary structure, it has traditionally been determined whether or not a particular peptide interacts with the target site of target protein by, for example, docking them using a molecular model and making an evaluation on an energy basis. To evaluate more peptides by such a technique, actually, for example, evaluation time per compound must be controlled up to about 1 minute in docking using a library comprising several thousands to several hundreds of thousands of low-molecular substances. However, because the number of variable portions of a peptide, even in the side chain only, is as many as up to 20, even for a 4-residue peptide, it took about 10 minutes per peptide to make an evaluation on Compac Alpha DS20E in, for example, flexible docking using AutoDock (see, for example, Journal of Computational Chemistry, vol. 19, p1639-1662 (1998)). For example, it is necessary to conduct docking 203, i.e., 8000 times, in the case of a 3-residue peptide, and 64,000,000 times in the case of a 6-residue peptide; exhaustive screening is actually extremely difficult.
For the reasons above, there has been a strong demand for the development of a technique for quickly designing a physiologically active peptide possessing excellent capability of binding to a target site of a protein.